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My question is this. If humans have 10 to 1 ratio of non-human to human living cells, could these bacteria/fungi or other forms actually be deadly for us IF we did not have an immune system developed?

Quite audacious isn't it. To some people it can be quite scary and to some, like myself, quite awe-inspiring. By physical cell counts humans are more microbe than human...[1]

As to your question, yes the bacteria and fungi in/on your body could be deadly IF we did not have an immune system. But it's a little more complicated than that.

Some bacteria are true pathogens i.e. they will cause disease when present, even in healthy individuals. These are bacteria like Shigella and Salmonella. They may not be deadly but they will cause disease. Then there are oppourtunistic pathogens which are usually quite docile, don't cause many problems when kept in check, but will cause disease if introduced into sterile areas or a compromised immune system. These include most bacteria i.e. Staphylococci, Streptococci, etc.

Now any way you look at it without an immune system you're screwed and dead in maybe a few days. But there are different levels of pathogenicity for bacteria. Some are badasses and highly pathogenic while most are mild-mannered and rarely cause problems.

And it's the mild-mannered ones that we owe our lives too. Without the bacteria on our skin, intestines, and respiratory tract we would die a pretty horrible death. The bacteria in our digestive system are largely responsible for processing carbohydrates and extracting energy. Along with this bacteria in our gut produce vitamins we couldn't normally produce. Besides this benefit the very presence of bacteria on our bodies creates a sort of protective layer and doesn't allow the very harmful bacteria to take hold and cause disease. They find it difficult to attach because someone is there first.

Additionally bacteria train our immune system in our very first days and months out of the womb. They talk to our cells with chemical messages. Encourage the healthy growth of our cells. Set up mutualistic colonies... I could go on. Point is: bacteria are important to us and keep us alive.

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Because if these organisms are indeed deadly without a functioning immune system to keep them at bay, that would mean that a designer came up with a disease and a disease fighting system, which then rules out a benevolent being for a designer.

A creator doesn't necessarily have to exist to design the pathogens. Evolution can provide the answers in an easier and more straight-forward approach. Humans and our human ancestors have been around for somewhere around 5 million years. Bacteria surely colonized the very first human to walk the Earth. And hence we have had 5 million years of mutual co-evolution together. But before that the ancestors to our human ancestors were probably colonized with billions of bacteria. And the ancestors of those ancestors of our human ancestors were colonized. Take it far enough back and eukaryotic cells and bacteria have been interacting with each other for somewhere around two billion years. In that span of time massive co-evolution has occurred.